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ArXiv May 2024Effective connectivity estimation plays a crucial role in understanding the interactions and information flow between different brain regions. However, the functional...
Effective connectivity estimation plays a crucial role in understanding the interactions and information flow between different brain regions. However, the functional time series used for estimating effective connectivity is derived from certain software, which may lead to large computing errors because of different parameter settings and degrade the ability to model complex causal relationships between brain regions. In this paper, a brain diffuser with hierarchical transformer (BDHT) is proposed to estimate effective connectivity for mild cognitive impairment (MCI) analysis. To our best knowledge, the proposed brain diffuser is the first generative model to apply diffusion models to the application of generating and analyzing multimodal brain networks. Specifically, the BDHT leverages structural connectivity to guide the reverse processes in an efficient way. It makes the denoising process more reliable and guarantees effective connectivity estimation accuracy. To improve denoising quality, the hierarchical denoising transformer is designed to learn multi-scale features in topological space. By stacking the multi-head attention and graph convolutional network, the graph convolutional transformer (GraphConformer) module is devised to enhance structure-function complementarity and improve the ability in noise estimation. Experimental evaluations of the denoising diffusion model demonstrate its effectiveness in estimating effective connectivity. The proposed model achieves superior performance in terms of accuracy and robustness compared to existing approaches. Moreover, the proposed model can identify altered directional connections and provide a comprehensive understanding of parthenogenesis for MCI treatment.
PubMed: 38168455
DOI: No ID Found -
Comparative Biochemistry and... Feb 2024Attempting to differentiate phenotypic variation caused by environmentally-induced alterations in gene expression from that caused by actual allelic differences can be...
Temperature and hypoxia trigger developmental phenotypic plasticity of cardiorespiratory physiology and growth in the parthenogenetic marbled crayfish, Procambarus virginalis Lyko, 2017.
Attempting to differentiate phenotypic variation caused by environmentally-induced alterations in gene expression from that caused by actual allelic differences can be experimentally difficult. Environmental variables must be carefully controlled and then interindividual genetic differences ruled out as sources of phenotypic variation. We investigated phenotypic variability of cardiorespiratory physiology as well as biometric traits in the parthenogenetically-reproducing marbled crayfish Procambarus virginalis Lyko, 2017, all offspring being genetically identical clones. Populations of P. virginalis were reared from eggs tank-bred at four different temperatures (16, 19, 22 and 25 °C) or two different oxygen levels (9.5 and 20 kPa). Then, at Stage 3 and 4 juvenile stages, physiological (heart rate, oxygen consumption) and morphological (carapace length, body mass) variables were measured. Heart rate and oxygen consumption measured at 23 °C showed only small effects of rearing temperature in Stage 3 juveniles, with larger effects evident in older, Stage 4 juveniles. Additionally, coefficients of variation were calculated to compare our data to previously published data on P. virginalis as well as sexually-reproducing crayfish. Comparison revealed that carapace length, body mass and heart rate (but not oxygen consumption) indeed showed lower, yet notable coefficients of variation in clonal crayfish. Yet, despite being genetically identical, significant variation in their morphology and physiology in response to different rearing conditions nonetheless occurred in marbled crayfish. This suggests that epigenetically induced phenotypic variation might play a significant role in asexual but also sexually reproducing species.
Topics: Animals; Astacoidea; Temperature; Parthenogenesis; Adaptation, Physiological; Hypoxia
PubMed: 38113959
DOI: 10.1016/j.cbpa.2023.111562 -
Molecular Plant Jan 2024
Topics: Apomixis; Crops, Agricultural; Seeds
PubMed: 38105558
DOI: 10.1016/j.molp.2023.12.010 -
Theriogenology Feb 2024Ellagic acid (EA) is a natural polyphenol and a free radical scavenger with antioxidant properties. This study investigated the protective effects of EA during in vitro...
Ellagic acid (EA) is a natural polyphenol and a free radical scavenger with antioxidant properties. This study investigated the protective effects of EA during in vitro maturation (IVM) of porcine oocytes. To determine the optimal concentration, IVM medium was supplemented with various concentrations of EA. Treatment with 10 μM EA (10 EA) resulted in the highest cleavage rate, blastocyst formation rate, and total cell number per blastocyst and the lowest percentage of apoptotic cell in parthenogenetic blastocysts. In the 10 EA group, abnormal spindle and chromosome misalignment were rescued and the ratio of phosphorylated p44/42 to total p44/42 was increased. Furthermore, the reactive oxygen species and glutathione levels were significantly decreased and increased, respectively, and antioxidant genes (Nrf2, HO-1, CAT, and SOD1) were significantly upregulated in the 10 EA group. mRNA expression of developmental-related (CDX2, POU5F1, and SOX2) and anti-apoptotic (BCL2L1) genes was significantly upregulated in the 10 EA group, while mRNA expression of pro-apoptotic genes (BAK, FAS, and CASP3) was significantly downregulated. Ultimately, following somatic cell nuclear transfer, the blastocyst formation rate was significantly increased and the percentage of apoptotic cell in blastocysts was significantly decreased in the 10 EA group. In conclusion, addition of 10 EA to IVM medium improved oocyte maturation and the subsequent embryo development capacity through antioxidant mechanisms. These findings suggest that EA can enhance the efficiencies of assisted reproductive technologies.
Topics: Swine; Animals; Antioxidants; Ellagic Acid; In Vitro Oocyte Maturation Techniques; Oocytes; Parthenogenesis; Embryonic Development; Blastocyst; Reactive Oxygen Species; RNA, Messenger
PubMed: 38100993
DOI: 10.1016/j.theriogenology.2023.12.001 -
Journal of Morphology Jan 2024Freshwater gastrotrichs have a biphasic lifecycle that reputedly involves the production of three types of eggs: apomictic and fast hatching (tachyblastic ova),...
Freshwater gastrotrichs have a biphasic lifecycle that reputedly involves the production of three types of eggs: apomictic and fast hatching (tachyblastic ova), apomictic and delayed hatching (opsiblastic ova), and plaque-bearing eggs (potentially derived from mixis). While some details of oogenesis and eggshell structure are known for tachyblastic ova, there are few details on other egg types. Here, we provide the first ultrastructural description of the oviposited opsiblastic eggs of the freshwater gastrotrich, Lepidodermella squamata. Scanning electron microscopy revealed the eggshell surface to be ornamented with long flattened pillar-like structures centered on polygonal plates that are pitted along their periphery. Transmission electron microscopy showed the pits to lead to a vast labyrinth of tubular spaces and larger cavities throughout the thick apical layer of the shell. The basal layer of the shell is amorphous and connected to a network of fine fibers that traverse an extra-oocyte space and forms a protective sheet around the uncleaved oocyte. The uncleaved oocyte has a dense layer of peripheral ooplasm surrounding a core of organelles including mitochondria, membrane-bound secretion granules, endoplasmic reticulum, and a single nucleus in a granular, ribosome-rich cytoplasm. Secretion granules are the most abundant organelles and presumably contain lipid-rich yolk that will be used as energy for delayed cleavage, thus functioning in temporal dispersal. These data are compared to the fine structure of invertebrate resting eggs across the phylogenetic spectrum to determine the novelty of opsiblastic egg structure in L. squamata.
Topics: Animals; Phylogeny; Oocytes; Oogenesis; Endoplasmic Reticulum; Fresh Water
PubMed: 38100746
DOI: 10.1002/jmor.21659 -
BioRxiv : the Preprint Server For... Dec 2023Bacteria in the genus have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing...
Bacteria in the genus have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called "parthenogenesis-induction" phenotype can be found in a number of strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 years ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex-determining factor Transformer, and a eukaryotic-like serine-threonine kinase with leucine rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model, . We suggest these proteins are parthenogenesis-inducing factors and our results indicate this would be made possible by a novel mechanism of bacterial-host interaction.
PubMed: 38076953
DOI: 10.1101/2023.12.01.569668 -
Phylloxera and Aphids Show Distinct Features of Genome Evolution Despite Similar Reproductive Modes.Molecular Biology and Evolution Dec 2023Genomes of aphids (family Aphididae) show several unusual evolutionary patterns. In particular, within the XO sex determination system of aphids, the X chromosome...
Genomes of aphids (family Aphididae) show several unusual evolutionary patterns. In particular, within the XO sex determination system of aphids, the X chromosome exhibits a lower rate of interchromosomal rearrangements, fewer highly expressed genes, and faster evolution at nonsynonymous sites compared with the autosomes. In contrast, other hemipteran lineages have similar rates of interchromosomal rearrangement for autosomes and X chromosomes. One possible explanation for these differences is the aphid's life cycle of cyclical parthenogenesis, where multiple asexual generations alternate with 1 sexual generation. If true, we should see similar features in the genomes of Phylloxeridae, an outgroup of aphids which also undergoes cyclical parthenogenesis. To investigate this, we generated a chromosome-level assembly for the grape phylloxera, an agriculturally important species of Phylloxeridae, and identified its single X chromosome. We then performed synteny analysis using the phylloxerid genome and 30 high-quality genomes of aphids and other hemipteran species. Unexpectedly, we found that the phylloxera does not share aphids' patterns of chromosome evolution. By estimating interchromosomal rearrangement rates on an absolute time scale, we found that rates are elevated for aphid autosomes compared with their X chromosomes, but this pattern does not extend to the phylloxera branch. Potentially, the conservation of X chromosome gene content is due to selection on XO males that appear in the sexual generation. We also examined gene duplication patterns across Hemiptera and uncovered horizontal gene transfer events contributing to phylloxera evolution.
Topics: Animals; Male; Aphids; X Chromosome; Parthenogenesis; Reproduction; Evolution, Molecular
PubMed: 38069672
DOI: 10.1093/molbev/msad271 -
Heredity Feb 2024From concatenated chromosomes to polyploidization, large-scale genome changes are known to occur in parthenogenetic animals. Here, we report mosaic aneuploidy in larval...
From concatenated chromosomes to polyploidization, large-scale genome changes are known to occur in parthenogenetic animals. Here, we report mosaic aneuploidy in larval brains of facultatively parthenogenetic Drosophila. We identified a background of aneuploidy in D. mercatorum strains and found increased levels of aneuploidy in the larval brain tissue of animals arising parthenogenetically versus those arising from sexual reproduction. There is also intra-individual variation in germline-derived aneuploidy within the same strain. To determine if this is a general feature of facultative parthenogenesis in drosophilids, we compared sexually reproduced and parthenogenetic offspring from an engineered facultative parthenogenetic strain of D. melanogaster. In addition to germline-derived aneuploidy, this revealed somatic aneuploidy that increased by up to fourfold in parthenogens compared to sexually reproduced offspring. Therefore, the genetic combination identified in D. mercatorum that causes facultative parthenogenesis in D. melanogaster results in aneuploidy, which indicates that the loss of mitotic control resulting in parthenogenesis causes subsequent genome variation within the parthenogenetic offspring. Our findings challenge the assumption that parthenogenetic offspring are near genetic replicas of their mothers.
Topics: Animals; Drosophila; Drosophila melanogaster; Reproduction; Sexual Behavior, Animal; Parthenogenesis
PubMed: 38017115
DOI: 10.1038/s41437-023-00664-z -
Syntenic relationship of chromosomes in species and based on the chromosome-level genome assemblies.Philosophical Transactions of the Royal... Jan 2024The clade, to which the parasitic nematode genus belongs, contains taxa with diverse lifestyles, ranging from free-living to obligate vertebrate parasites....
The clade, to which the parasitic nematode genus belongs, contains taxa with diverse lifestyles, ranging from free-living to obligate vertebrate parasites. Reproductive strategies are also diverse in this group of nematodes, employing not only sexual reproduction but also parthenogenesis, making it an attractive group to study genome adaptation to specific conditions. An in-depth understanding of genome evolution, however, has been hampered by fragmented genome assemblies. In this study, we generated chromosome-level genome assemblies for two species and the outgroup species using long-read sequencing and high-throughput chromosome conformation capture (Hi-C). Our synteny analyses revealed a clearer picture of chromosome evolution in this group, suggesting that a functional sex chromosome has been maintained throughout the group. We further investigated sex chromosome dynamics in the lifecycle of and found that bivalent formation in oocytes appears to be important for male production in the mitotic parthenogenesis. This article is part of the Theo Murphy meeting issue ': omics to worm-free populations'.
Topics: Animals; Male; Strongyloides; Synteny; Chromosomes; Nematoda; Life Cycle Stages; Sex Chromosomes
PubMed: 38008120
DOI: 10.1098/rstb.2022.0446 -
Theriogenology Feb 2024In vitro maturation (IVM) methods for porcine oocytes are still deficient in achieving full developmental capacity, as the currently available oocyte in vitro culture...
Three-dimensional glass scaffolds improve the In Vitro maturation of porcine cumulus-oocyte complexes and subsequent embryonic development after parthenogenetic activation.
In vitro maturation (IVM) methods for porcine oocytes are still deficient in achieving full developmental capacity, as the currently available oocyte in vitro culture systems still have limitations. In vitro embryo production must also improve the porcine oocyte IVM system to acquire oocytes with good developmental potential. Herein, we tested a three-dimensional (3D) glass scaffold culture system for porcine oocyte maturation. After 42 h, we matured porcine cumulus-oocyte complexes (COCs) on either two-dimensional glass dishes (2D-B), two-dimensional microdrops (2D-W), or 3D glass scaffolds. The 3D glass scaffolds were tested for porcine oocyte maturation and embryonic development. Among these culture methods, the extended morphology of the 3D group maintained a 3D structure better than the 2D-B and 2D-W groups, which had flat COCs that grew close to the bottom of the culture vessel. The COCs of the 3D group had a higher cumulus expansion index and higher first polar body extrusion rate, cleavage rate, and blastocyst rate of parthenogenetic embryos than the 2D-B group. In the 3D group, the cumulus-expansion-related gene HAS2 and anti-apoptotic gene Bcl-2 were significantly upregulated (p < 0.05), while the pro-apoptotic gene Caspase3 was significantly downregulated (p < 0.05). The blastocysts of the 3D group had a higher relative expression of Bcl-2, Oct4, and Nanog than the other two groups (p < 0.05). The 3D group also had a more uniform distribution of mitochondrial membrane potential and mitochondria (p < 0.05), and its cytoplasmic active oxygen species content was much lower than that in the 2D-B group (p < 0.05). These results show that 3D glass scaffolds dramatically increased porcine oocyte maturation and embryonic development after parthenogenetic activation, providing a suitable culture model for porcine oocytes.
Topics: Pregnancy; Female; Swine; Animals; Oocytes; Embryonic Development; In Vitro Oocyte Maturation Techniques; Parthenogenesis; Blastocyst; Proto-Oncogene Proteins c-bcl-2; Cumulus Cells
PubMed: 38008049
DOI: 10.1016/j.theriogenology.2023.11.011